Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease

Abstract

Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn’s disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBDs have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of IBDs and dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identified a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward towards understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBDs.

The role of gut microbiome in inflammatory bowel disease diagnosis and prognosis

“… 57 By assessing 20 bacteria markers in mucosal samples from Chilean and Spanish patients with IBD, Chamorro et al. 58 were able to discriminate dysbiosis and eubiosis in IBD patients, with an AUC ranging from 0.96 to 0.99.…”

“…Using only 11 mucosal bacteria, Chamorro et al. 58 could differentiate UC from CD with an AUC of 0.83. These findings suggest the possibility of using a specific set of microbes for IBD subtype classification.…”

“…Studies have used fecal or mucosal bacteria signatures to distinguish UC from CD.Manandhar et al53 identified 117 differential bacterial taxa from stool samples for discriminating CD with UC which showed excellent performance (AUC >0.90). Using only 11 mucosal bacteria, Chamorro et al58 could differentiate UC from CD with an AUC of 0.83. These…”

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“…When identity values were <98.7 and >94.5% with the closest relative type strain, reads were different unclassified species of the same genus [ 20 ]. This focus uses phylogenetic inference rather than clustering by sequence identity to show diversity measures as group sequences in lineages that approach the species thresholds with a more robust view of microbial diversity [ 21 ].…”

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